A test of the loose-equilibrium concept with long-lived organisms: Evaluating temporal change in freshwater mussel assemblages.

The loose-equilibrium concept (LEC) predicts that ecological assemblages change transiently but return towards an earlier or average structure. The LEC framework can help determine whether assemblages vary within expected ranges or are permanently altered following environmental change. Long-lived, slow-growing animals typically respond slowly to environmental change, and their assemblage dynamics may respond over decades, which transcends most ecological studies. Unionid mussels are valuable for studying dynamics of long-lived animals because they can live >50 years and occur in dense, species-rich assemblages (mussel beds). Mussel beds can persist for decades, but disturbance can affect species differently, resulting in variable trajectories according to differences in species composition within and among rivers. We used long-term data sets (10-40 years) from seven rivers in the eastern United States to evaluate the magnitude, pace and directionality of mussel assemblage change within the context of the LEC. Site trajectories varied within and among streams and showed patterns consistent with either the LEC or directional change. In streams that conformed to the LEC, rank abundance of dominant species remained stable over time, but directional change in other streams was driven by changes in the rank abundance and composition of dominant species. Characteristics of mussel assemblage change varied widely, ranging from those conforming to the LEC to those showing strong directional change. Conservation approaches that attempt to maintain or create a desired assemblage condition should acknowledge this wide range of possible assemblage trajectories and that the environmental factors that influence those changes remain poorly understood.

Multi-year weed community dynamics and rice yields as influenced by tillage, crop establishment, and weed control: Implications for rice-maize rotations in the eastern Gangetic plains.

In South Asia's rice-based cropping systems, most farmers flood and repetitively till their fields before transplanting. This establishment method, commonly termed puddled transplanted rice (TPR), is costly. In addition, it is labor and energy intensive. To increase labor and energy efficiency in rice production, reduced or zero-tilled direct seeded rice (ZT-DSR) is commonly proposed as an alternative tillage and crop establishment (TCE) option. Effective management of weeds in ZT-DSR however remains a major challenge. We conducted a four-year experiment under a rice-maize rotation in Northwestern Bangladesh in the eastern Gangetic Plains to examine the performance of two TCE methods and three weed management regimes (WMR) on the diversity and competitiveness of weed communities in the rice phase of the rotation. The Shannon-Weiner Diversity Index, a measure of species diversity, was significantly greater under ZT-DSR than puddled TPR. It was also greater under no weed control (Weedy) and two manual weeding (MW) treatments compared to chemical herbicide with manual weeding (C + MW). In DSR Weedy plots, weed communities began shifting from grasses to sedges from the rotation's second year, while in the ZT-DSR and C + MW treatments, sedges were consistently predominant. In both puddled TPR Weedy and TPR C + MW treatments, broadleaves and grasses were dominant in the initial year, while sedges dominated in the final year. There were significant main effects of year (Y) and weed management regime (WMR), but not of TCE. Significant Y × TCE and TCE × WMR interaction effects on rice yield were also observed. Grain yields under ZT-DSR were similar to puddled TPR. ZT-DSR with one application of pre-emergence herbicide followed by one hand weeding at 28 days after establishment however resulted in significantly higher grain yield (5.34 t ha-1) compared the other weed management regimes. Future research should address methods to effectively manage weed community composition shifts in both ZT-DSR and TPR under rice-maize rotations utilizing integrated and low-cost strategies that can be readily applied by farmers in the eastern Gangetic Plains.

Abundance Inequality in Freshwater Communities Has an Ecological Origin.

The hollow-shaped species abundance distribution (SAD) and its allied rank abundance distribution (RAD)-showing that abundance is unevenly distributed among species-are some of the most studied patterns in ecology. To explain the nature of abundance inequality, I developed a novel framework identifying environmental favorability, which controls the balance between reproduction and immigration, as the ultimate source and species stress tolerance as a proximate factor. Thus, under harsh conditions, only a few tolerant species can reproduce, while some sensitive species can be present in low numbers due to chance immigration. This would lead to high abundance inequality between the two groups of species. Under benign conditions, both groups can reproduce and give rise to higher abundance equality. To test these ideas, I examined the variability in the parameters of a Poisson lognormal fit of the SAD and a square root fit of the RAD in diatom and fish communities across US streams. Indeed, as environmental favorability increased, more sensitive forms were able to establish large populations, diminishing the abundance disparity between locally common and rare species. Finally, it was demonstrated that in diatoms, the RAD belonged to the same family of relationships as those of population density with body size and regional distribution.

Effects of land-use intensity on arthropod species abundance distributions in grasslands.

As a rule, communities consist of few abundant and many rare species, which is reflected in the characteristic shape of species abundance distributions (SADs). The processes that shape these SADs have been a longstanding problem for ecological research. Although many studies found strong negative effects of increasing land-use intensity on diversity, few reports consider land-use effects on SADs. Arthropods (insects and spiders) were sampled on 142 grassland plots in three regions in Germany, which were managed with different modes (mowing, fertilization and/or grazing) and intensities of land use. We analysed the effect of land use on three parameters characterizing the shape of SADs: abundance decay rate (the steepness of the rank abundance curve, represented by the niche-preemption model parameter), dominance (Berger-Parker dominance) and rarity (Fisher's alpha). Furthermore, we tested the core-satellite hypothesis by comparing the species' rank within the SAD to their distribution over the land-use gradient. When data on Araneae, Cicadina, Coleoptera, Heteroptera and Orthoptera were combined, abundance decay rate increased with combined land-use intensity (including all modes). Among the single land-use modes, increasing fertilization and grazing intensity increased the decay rate of all taxa, while increasing mowing frequency significantly affected the decay rate only in interaction with fertilization. Results of single taxa differed in their details, but all significant interaction effects included fertilization intensity. Dominance generally increased with increasing fertilization and rarity decreased with increasing grazing or mowing intensity, despite small differences among taxa and regions. The majority of species found on <10% of the plots per region were generally rare (<10 individuals), which is in accordance with the core-satellite hypothesis. We found significant differences in the rarity and dominance of species between plots of low and high intensity for all three land-use modes and for the combined land-use intensity. We conclude that effects of land-use intensity on SADs lead to a stronger dominance of the most abundant species. Furthermore, species which have restricted distributions are more likely to also be rare species in the local SAD and therefore are at high risk of being lost under intensive land use.

Measuring ß-diversity with species abundance data.

In 2003, 24 presence-absence ß-diversity metrics were reviewed and a number of trade-offs and redundancies identified. We present a parallel investigation into the performance of abundance-based metrics of ß-diversity. ß-diversity is a multi-faceted concept, central to spatial ecology. There are multiple metrics available to quantify it: the choice of metric is an important decision. We test 16 conceptual properties and two sampling properties of a ß-diversity metric: metrics should be 1) independent of α-diversity and 2) cumulative along a gradient of species turnover. Similarity should be 3) probabilistic when assemblages are independently and identically distributed. Metrics should have 4) a minimum of zero and increase monotonically with the degree of 5) species turnover, 6) decoupling of species ranks and 7) evenness differences. However, complete species turnover should always generate greater values of ß than extreme 8) rank shifts or 9) evenness differences. Metrics should 10) have a fixed upper limit, 11) symmetry (ßA,B  = ßB,A ), 12) double-zero asymmetry for double absences and double presences and 13) not decrease in a series of nested assemblages. Additionally, metrics should be independent of 14) species replication 15) the units of abundance and 16) differences in total abundance between sampling units. When samples are used to infer ß-diversity, metrics should be 1) independent of sample sizes and 2) independent of unequal sample sizes. We test 29 metrics for these properties and five 'personality' properties. Thirteen metrics were outperformed or equalled across all conceptual and sampling properties. Differences in sensitivity to species' abundance lead to a performance trade-off between sample size bias and the ability to detect turnover among rare species. In general, abundance-based metrics are substantially less biased in the face of undersampling, although the presence-absence metric, ßsim , performed well overall. Only ßBaselga R turn , ßBaselga B-C turn and ßsim measured purely species turnover and were independent of nestedness. Among the other metrics, sensitivity to nestedness varied >4-fold. Our results indicate large amounts of redundancy among existing ß-diversity metrics, whilst the estimation of unseen shared and unshared species is lacking and should be addressed in the design of new abundance-based metrics.

Competition model explains trends of long-term fertilization in plant communities.

Over 40 years ago, Kempton (Biometrics, 35, 1979, 307) reported significant modification to plant community structure following a long-term fertilization experiment. Many researchers have investigated this phenomenon in the years since. Collectively, these studies have shown consistent shifts in rank abundance relationships among species in communities following fertilization. The previous studies indicated that fertilization affects community structure through several critical processes, including trait-based functional response, reordering of species in rank abundance diagram (RAD), and niche dimensionality, although some questions have remained. How does the species reordering driven by the plant responses cause characteristic trends in temporal changes of RAD? Why are those trends ubiquitous in various systems? To answer those questions, we theoretically investigated the effects of fertilization on community structure based on a colonization model (or Levins model) with competition-fecundity trade-offs, which can result in the coexistence of multiple species under competition. The model represents characteristic RAD, which can be an adequate tool to study community composition. Our theoretical model comprehensively represents observed trends in rank abundance relationships following long-term fertilization and suggests that competitive interactions among species are a critical factor in structuring species diversity in plant communities.

Impacts of a novel controlled-release TiO2-coated (nano-) formulation of carbendazim and its constituents on freshwater macroinvertebrate communities.

Recently, the delivery of pesticides through novel controlled-release (nano-)formulations has been proposed intending to reduce (incidental) pesticide translocation to non-target sites. Concerns have however been raised with regards to the potentially enhanced toxicity of controlled-release (nano-)formulations to non-target organisms and ecosystems. We evaluated long-term (i.e. 1 and 3 month-) impacts of a novel controlled-release pesticide formulation (nano-TiO2-coated carbendazim) and its individual and combined constituents (i.e. nano-sized TiO2 and carbendazim) on naturally established freshwater macroinvertebrate communities. In doing so, we simultaneously assessed impacts of nano-sized TiO2 (nTiO2), currently one of the most used and emitted engineered nanomaterials world-wide. We determined ecological impacts on diversity (i.e. ß-diversity), structure (i.e. rank abundance parameters), and functional composition (i.e. feeding guilds & trophic groups) of communities and underlying effects at lower organizational levels (i.e. population dynamics of individual taxa). Freshwater macroinvertebrate communities were negligibly impacted by nTiO2 at environmentally realistic concentrations. The controlled-release (nano-)formulation significantly delayed release of carbendazim to the water column. Nevertheless, conventional- (i.e. un-coated-) and nTiO2-coated carbendazim induced a similar set of adverse impacts at all investigated levels of ecological organization and time points. Our findings show fundamental restructuring of the taxonomic- and functional composition of macroinvertebrate communities as a result of low-level pesticide exposure, and thereby highlight the need for mitigating measures to reduce pesticide-induced stress on freshwater ecosystems.

Tracking the upstream history of aquatic microbes in a boreal lake yields new insights on microbial community assembly.

Bacterial community structure can change rapidly across short spatial and temporal scales as environmental conditions vary, but the mechanisms underlying those changes are still poorly understood. Here, we assessed how a lake microbial community assembles by following its reorganization from the main tributary, which, when flowing into the lake, first traverses an extensive macrophyte-dominated vegetated habitat, before reaching the open water. Environmental conditions in the vegetated habitat changed drastically compared to both river and lake waters and represented a strong environmental gradient for the incoming bacteria. We used amplicon sequencing of the 16S rRNA gene and transcript to reconstruct the shifts in relative abundance of individual taxa and link this to their pattern in activity (here assessed with RNA:DNA ratios). Our results indicate that major shifts in relative abundance were restricted mostly to rare taxa (<0.1% of relative abundance), which seemed more responsive to environmental changes. Dominant taxa (>1% of relative abundance), on the other hand, traversed the gradient mostly unchanged with relatively low and stable RNA:DNA ratios. We also identified a high level of local recruitment and a seedbank of taxa capable of activating/inactivating, but these were almost exclusively associated with the rare biosphere. Our results suggest a scenario where the lake community results from a reshuffling of the rank abundance structure within the incoming rare biosphere, driven by selection and growth, and that numerical dominance is not a synonym of activity, growth rate, or environmental selection, but rather reflect mass effects structuring these freshwater bacterial communities.

Colonization process determines species diversity via competitive quasi-exclusion.

A colonization model provides a useful basis to investigate a role of interspecific competition in species diversity. The model formulates colonization processes of propagules competing for spatially distinct habitats, which is known to result in stable coexistence of multiple species under various trade-off, for example, competition-colonization and fecundity-mortality trade-offs. Based on this model, we propose a new theory to explain patterns of species abundance, assuming a trade-off between competitive ability and fecundity among species. This model makes testable predictions about species positions in the rank abundance diagram under a discrete species competitiveness. The predictions were tested by three data of animal communities, which supported our model, suggesting the importance of interspecific competition in community structure. Our approach provides a new insight into understanding a mechanism of species diversity.

Botanic gardens are an untapped resource for studying the functional ecology of tropical plants.

Functional traits are increasingly used to understand the ecology of plants and to predict their responses to global changes. Unfortunately, trait data are unavailable for the majority of plant species. The lack of trait data is especially prevalent for hard-to-measure traits and for tropical plant species, potentially owing to the many inherent difficulties of working with species in remote, hyperdiverse rainforest systems. The living collections of botanic gardens provide convenient access to large numbers of tropical plant species and can potentially be used to quickly augment trait databases and advance our understanding of species' responses to climate change. In this review, we quantitatively assess the availability of trait data for tropical versus temperate species, the diversity of species available for sampling in several exemplar tropical botanic gardens and the validity of garden-based leaf and root trait measurements. Our analyses support the contention that the living collections of botanic gardens are a valuable scientific resource that can contribute significantly to research on plant functional ecology and conservation.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.

The spatial organization and microbial community structure of an epilithic biofilm.

Microbial biofilms are common on lithic surfaces, including stone buildings. However, the ecology of these communities is poorly understood. Few studies have focused on the spatial characteristics of lithobiontic biofilms, despite the fact that spatial structure has been demonstrated to influence ecosystem function (and hence biodegradation) and community diversity. Furthermore, relatively few studies have utilized molecular techniques to characterize these communities, even though molecular methods have revealed unexpected microbial diversity in other habitats. This study investigated (1) the spatial structure and (2) the taxonomic composition of an epilithic biofilm using molecular techniques, namely amplicon pyrosequencing and terminal restriction fragment length polymorphism. Dispersion indices and Mantel correlograms were used to test for the presence of spatial structure in the biofilm. Diversity metrics and rank-abundance distributions (RADs) were also generated. The study revealed spatial structure on a centimetre scale in eukaryotic microbes (fungi and algae), but not the bacteria. Fungal and bacterial communities were highly diverse; algal communities much less so. The RADs were characterized by a distinctive 'hollow' (concave up) profile and long tails of rare taxa. These findings have implications for understanding the ecology of epilithic biofilms and the spatial heterogeneity of stone biodeterioration.